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Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori

van Vliet, Arnoud (2016) Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori FEMS Microbiology Letters, 364 (2), fnw296..

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Abstract

The human bacterial pathogen Helicobacter pylori has a highly variable genome, with significant allelic and sequence diversity between isolates and even within well-characterised strains, hampering comparative genomics of H. pylori. In this study, pan-genome analysis has been used to identify lineage-specific genes of H. pylori. A total of 346 H. pylori genomes spanning the hpAfrica1, hpAfrica2, hpAsia2, hpEurope, hspAmerind and hspEAsia multilocus sequence typing (MLST) lineages were searched for genes specifically over- or underrepresented in MLST lineages or associated with the cag pathogenicity island (PAI). The only genes overrepresented in cagpositive genomes were the cag PAI genes themselves. In contrast, a total of 125 genes were either overrepresented or underrepresented in one or more MLST-lineages. Of these 125 genes, alcohol/aldehyde-reducing enzymes linked with acid-resistance and production of toxic aldehydes were found to be overrepresented in African lineages. Conversely, the FecA2 ferric citrate receptor was missing from hspAmerind genomes, but present in all other lineages. This work shows the applicability of pan-genome analysis for identification of lineage-specific genes of H. pylori, facilitating further investigation to allow linkage of differential distribution of genes with disease outcome or virulence, and can be used with other microbial pathogens with highly variable genomes.

Item Type: Article
Subjects : Veterinary Medicine
Divisions : Faculty of Health and Medical Sciences > School of Veterinary Medicine
Authors :
NameEmailORCID
van Vliet, Arnouda.vanvliet@surrey.ac.ukUNSPECIFIED
Date : 23 December 2016
Identification Number : 10.1093/femsle/fnw296
Copyright Disclaimer : This is a pre-copyedited, author-produced version of an article accepted for publication in FEMS Microbiology Letters, following peer review. The version of record Arnoud H. M. van Vliet; Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori. FEMS Microbiol Lett 2017; 364 (2): fnw296. doi: 10.1093/femsle/fnw296 is available online at: https://academic.oup.com/femsle/article/2735779
Uncontrolled Keywords : Helicobacter pylori, comparative genomics, multilocus sequence typing, genome sequences, pan-genome analysis
Related URLs :
Depositing User : Symplectic Elements
Date Deposited : 03 Jan 2017 14:43
Last Modified : 07 Jul 2017 11:21
URI: http://epubs.surrey.ac.uk/id/eprint/813183

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